I didn't quite get it... 0.005% of what? Profit on sales in Ireland? Profit on sales in other parts of the world?
Are people complaining that when Apple sells a phone in Italy, Ireland taxes that at zero? Is that the complaint?
The issue is that the normal tax rate in Ireland is around 12%, and Apple uses accounting tricks and tax exceptions to lower their effective tax rate there to 0.005%. That is the part that the the European Commission ruled illegal.
In Ireland, they argue that the profits happen at a "head office" which was not based in any country and did not have any employees or own premises.
(The ruling: http://ec.europa.eu/competition/state_aid/cases/253200/25320... linked from http://ec.europa.eu/competition/elojade/isef/case_details.cf...) - search for "AOI"